Histological analysis is widely applied to archaeological and fossil bones in order to identify diagenetic changes in bone microstructure. Diagenetic processes, affecting bones from the body deposition to the discovery, strongly depend on environmental conditions; therefore the study of diagenetic alterations provides valuable information on the taphonomic history of bones and on their burial environment. Histological analysis was performed on 58 samples of human compact bone found at Al Khiday (Khartoum, Sudan), a multi-stratified archaeological site that revealed a cemetery with distinct burial phases dating from the Early Holocene to the II century AD. The well-defined archaeological context provides a set of bone samples belonging to the same site but buried in different phases and under different environmental conditions: Central Sudan was characterized by a humid environment with seasonal swamp and palaeo-lakes in the Early Holocene, while in the II century AD the environmental conditions were more similar to the current arid climate of the Sub-Saharan belt. Scanning electron microscopy and high-resolution X-ray computed micro-tomography analysis revealed extensive bacterial and fungal attack, and secondary phases precipitation and dissolution in the samples. The analysis of textural relationships between each diagenetic feature enabled to establish a relative chronological sequence of the events acting during burial. Moreover different patterns of diagenetic alterations were observed for burial phases of different ages, proving a strong relationship between diagenesis and the environmental conditions.